I’m having similar issues to the referenced link. I’m getting a Skip to content text using IE9/IE10/IE11. Using IETester to validate using other IE versions. Oddly on my local desktop using IE11 it does not happen. But I’ve gotten the Skip to content issue on several other desktops.
I already tried adding the gistfile1.php code into functions.php, but that didn’t fix it.
I was browse http://whatsnew (internal) and it would render differently than using FQDN.
Turns out it has something to do with IE compatibility mode for Display intranet sites in Compatibility View setting. I had to add this line below in the <head> (keep in mind that it has to be near the top of the <head>.
It basically forces your IE to use the newest rendering mode.